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Issue with Phasing in AlphaImpute2 #28

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jsleper opened this issue Dec 4, 2023 · 1 comment
Open

Issue with Phasing in AlphaImpute2 #28

jsleper opened this issue Dec 4, 2023 · 1 comment

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@jsleper
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jsleper commented Dec 4, 2023

I have been running AlphaImpute2 today. Regardless of what datasets I use (my own or the example provided in the GitHub package), I am receiving the same error message. I took a screenshot below. Basically, the imputation seems to run ok and writes a .genotype file, but the phasing always errors out at the very end and will not write the .phase file. My inputs are just a genotype and pedigree file and with -phase_output keyed in.

Below is the example:

AlphaImpute2 -genotypes ./AlphaImpute2-main/example/data/genotypes.txt -pedigree ./AlphaImpute2-main/example/data/pedigree.txt -out test -phase_output

I get the error AttributeError: 'tuple' has no attribute 'ndim'. The files are simply the example files in the package. I can provide others if needed, but figured this the example files are a good start.

Any help would be much appreciated!

Josh

@gregorgorjanc
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The same as #16

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